As far as I have been able to tell the breakage seems to be introduced with 
the
new X11 in Lion. The molmol program built either under SL and run under Lion or
built under Lion fails to display the widgets or menus in its windows. The 
current
bahavior looks a lot like something we saw on MacPorts previously...

https://trac.macports.org/ticket/21835

Perhaps the problem resurfaced again. Unfortunately it was never determined 
exactly
what change to the xorg packages solved the problem.
             Jack

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